toil 8.0.0__py3-none-any.whl → 8.1.0b1__py3-none-any.whl

toil/worker.py

@@ -11,6 +11,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+import atexit
 import base64
 import copy
 import json
@@ -22,7 +23,9 @@ import shutil
 import signal
 import socket
 import stat
+import subprocess
 import sys
+import threading
 import time
 import traceback
 from collections.abc import Iterator
@@ -59,7 +62,6 @@ class StatsDict(MagicExpando):
 
     jobs: list[MagicExpando]
 
-
 def nextChainable(
     predecessor: JobDescription, job_store: AbstractJobStore, config: Config
 ) -> Optional[JobDescription]:
@@ -165,6 +167,85 @@ def nextChainable(
     # Made it through! This job is chainable.
     return successor
 
+def unstick_worker(interval: float = 120, timeout: float = 120) -> None:
+    """
+    Thread function that tries to prevent the process from getting stuck.
+
+    Meant to be used as a daemon thread: does not have a shutdown signal but
+    cleans up on exit.
+
+    :param interval: Try to unstick the process at intervals of this many
+        seconds.
+    :param timeout: Stop child processes that take longer than this many
+        seconds to finish.
+    """
+
+    # We've observed Toil getting stuck reading the job from the job store,
+    # either due to a problem with the FileJobStore or with local temp storage,
+    # but then get unstuck as soon as someone logged in and ran lsof on the
+    # Toil process. So we make sure to do that to ourselves every once in a
+    # while as long as the worker is running.
+
+    # Figure out our process ID
+    pid = os.getpid()
+
+    child: Optional[subprocess.Popen[bytes]] = None
+
+    def clean_up_child() -> None:
+        """
+        Cleanup function to run at daemon thread shutdown when the main thread
+        terminates without shutting us down.
+
+        Also used to kill the child process if it takes too long.
+        """
+        if child is not None:
+            # Kill the child immediately if it is running
+            child.kill()
+            try:
+                # Wait one last time to try and reap the child process
+                child.wait(timeout=5)
+            except subprocess.TimeoutExpired:
+                pass
+
+    atexit.register(clean_up_child)
+
+    # TODO: If we handle daemon thread shutdown just fine, why do we bother
+    # with all the event stuff? Why not cut it?
+
+    # Wait the interval before trying the first unstick
+    time.sleep(interval)
+
+    while True:
+        # Run an lsof on our PID, which has been observed to unstick reads.
+        #
+        # We rely on the thread being able to go away and atexit() hooks
+        # happening in the middle of a wait with a timeout.
+        #
+        # We also want to handle the case where the child process gets so
+        # gummed up that it can't exit when killed.
+
+        # Preserve errors form child process but not output
+        child = subprocess.Popen(
+            ["lsof", "-p", str(pid)],
+            stdin=subprocess.DEVNULL,
+            stdout=subprocess.DEVNULL,
+        )
+        try:
+            child.wait(timeout=timeout)
+        except subprocess.TimeoutExpired:
+            logger.warning("Running lsof took too long!")
+            clean_up_child()
+            if child.returncode is None:
+                # Kill didn't take
+                logger.warning("Could not promptly kill child process: %s", child.pid)
+
+        if child.returncode != 0:
+            # Something went wrong, which is suspicious. Either it failed or it
+            # timed out and could not be killed promptly.
+            logger.warning("Could not list open files on ourselves. Return code: %s", child.returncode)
+
+        # Wait the interval.
+        time.sleep(interval)
 
 def workerScript(
     job_store: AbstractJobStore,
@@ -240,6 +321,13 @@ def workerScript(
         # We don't need to reap the child. Either it kills us, or we finish
         # before it does. Either way, init will have to clean it up for us.
 
+    ##########################################
+    # Create the worker unsticker
+    ##########################################
+    unstick_thread = threading.Thread(target=unstick_worker, args=())
+    unstick_thread.daemon = True
+    unstick_thread.start()
+
     ##########################################
     # Load the environment for the job
     ##########################################
@@ -443,13 +531,12 @@ def workerScript(
                 )
 
         ##########################################
-        # Setup the stats, if requested
+        # Setup the stats
         ##########################################
 
-        if config.stats:
-            # Remember the cores from the first job, which is how many we have reserved for us.
-            statsDict.workers.requested_cores = jobDesc.cores
-            startClock = ResourceMonitor.get_total_cpu_time()
+        # Remember the cores from the first job, which is how many we have reserved for us.
+        statsDict.workers.requested_cores = jobDesc.cores
+        startClock = ResourceMonitor.get_total_cpu_time()
 
         startTime = time.time()
         while True:
@@ -483,7 +570,7 @@ def workerScript(
                 )
                 try:
                     with job._executor(
-                        stats=statsDict if config.stats else None, fileStore=fileStore
+                        stats=statsDict, fileStore=fileStore
                     ):
                         with deferredFunctionManager.open() as defer:
                             with fileStore.open(job):
@@ -594,22 +681,21 @@ def workerScript(
         ##########################################
         # Finish up the stats
         ##########################################
-        if config.stats:
-            totalCPUTime, totalMemoryUsage = (
-                ResourceMonitor.get_total_cpu_time_and_memory_usage()
-            )
-            statsDict.workers.time = str(time.time() - startTime)
-            statsDict.workers.clock = str(totalCPUTime - startClock)
-            statsDict.workers.memory = str(totalMemoryUsage)
-            # Say the worker used the max disk we saw from any job
-            max_bytes = 0
-            for job_stats in statsDict.jobs:
-                if "disk" in job_stats:
-                    max_bytes = max(max_bytes, int(job_stats.disk))
-            statsDict.workers.disk = str(max_bytes)
-            # Count the jobs executed.
-            # TODO: toil stats could compute this but its parser is too general to hook into simply.
-            statsDict.workers.jobs_run = len(statsDict.jobs)
+        totalCPUTime, totalMemoryUsage = (
+            ResourceMonitor.get_total_cpu_time_and_memory_usage()
+        )
+        statsDict.workers.time = str(time.time() - startTime)
+        statsDict.workers.clock = str(totalCPUTime - startClock)
+        statsDict.workers.memory = str(totalMemoryUsage)
+        # Say the worker used the max disk we saw from any job
+        max_bytes = 0
+        for job_stats in statsDict.jobs:
+            if "disk" in job_stats:
+                max_bytes = max(max_bytes, int(job_stats.disk))
+        statsDict.workers.disk = str(max_bytes)
+        # Count the jobs executed.
+        # TODO: toil stats could compute this but its parser is too general to hook into simply.
+        statsDict.workers.jobs_run = len(statsDict.jobs)
 
         # log the worker log path here so that if the file is truncated the path can still be found
         if redirect_output_to_log_file:
@@ -767,16 +853,10 @@ def workerScript(
         statsDict.logs.names = [names.stats_name for names in jobDesc.get_chain()]
         statsDict.logs.messages = logMessages
 
-    if (
-        debugging
-        or config.stats
-        or statsDict.workers.logs_to_leader
-        or statsDict.workers.logging_user_streams
-    ):
-        # We have stats/logging to report back.
-        # We report even if the job attempt failed.
-        # TODO: Will that upset analysis of the stats?
-        job_store.write_logs(json.dumps(statsDict, ensure_ascii=True))
+    # We have stats/logging to report back.
+    # We report even if the job attempt failed.
+    # TODO: Will that upset analysis of the stats?
+    job_store.write_logs(json.dumps(statsDict, ensure_ascii=True))
 
     # Remove the temp dir
     cleanUp = config.cleanWorkDir

{toil-8.0.0.dist-info → toil-8.1.0b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: toil
-Version: 8.0.0
+Version: 8.1.0b1
 Summary: Pipeline management software for clusters.
 Home-page: https://github.com/DataBiosphere/toil
 Author: Benedict Paten and the Toil community
@@ -37,7 +37,7 @@ Requires-Dist: requests<=2.31.0
 Requires-Dist: docker<8,>=6.1.0
 Requires-Dist: urllib3<3,>=1.26.0
 Requires-Dist: python-dateutil
-Requires-Dist: psutil<7,>=6.1.0
+Requires-Dist: psutil<8,>=6.1.0
 Requires-Dist: PyPubSub<5,>=4.0.3
 Requires-Dist: addict<2.5,>=2.2.1
 Requires-Dist: backports.zoneinfo[tzdata]; python_version < "3.9"
@@ -47,6 +47,7 @@ Requires-Dist: ruamel.yaml>=0.15
 Requires-Dist: pyyaml<7,>=6
 Requires-Dist: typing-extensions<5,>=4.6.2
 Requires-Dist: coloredlogs<16,>=15
+Requires-Dist: prompt_toolkit<4,>=3.0
 Provides-Extra: aws
 Requires-Dist: boto3-stubs[autoscaling,boto3,ec2,iam,s3,sdb,sts]<2,>=1.28.3.post2; extra == "aws"
 Requires-Dist: mypy-boto3-iam<2,>=1.28.3.post2; extra == "aws"
@@ -83,7 +84,7 @@ Provides-Extra: server
 Requires-Dist: connexion[swagger-ui]<4,>=2.10.0; extra == "server"
 Requires-Dist: flask<4,>=2.0; extra == "server"
 Requires-Dist: werkzeug<4,>=2.0; extra == "server"
-Requires-Dist: flask-cors==5.0.0; extra == "server"
+Requires-Dist: flask-cors==5.0.1; extra == "server"
 Requires-Dist: gunicorn==23.0.0; extra == "server"
 Requires-Dist: celery<6,>=5.1.0; extra == "server"
 Requires-Dist: wes-service<5,>=4.0.0; extra == "server"
@@ -122,7 +123,7 @@ Requires-Dist: graphlib-backport==1.0; python_version < "3.9" and extra == "all"
 Requires-Dist: connexion[swagger-ui]<4,>=2.10.0; extra == "all"
 Requires-Dist: flask<4,>=2.0; extra == "all"
 Requires-Dist: werkzeug<4,>=2.0; extra == "all"
-Requires-Dist: flask-cors==5.0.0; extra == "all"
+Requires-Dist: flask-cors==5.0.1; extra == "all"
 Requires-Dist: gunicorn==23.0.0; extra == "all"
 Requires-Dist: celery<6,>=5.1.0; extra == "all"
 Requires-Dist: wes-service<5,>=4.0.0; extra == "all"
@@ -140,6 +141,10 @@ Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 
+.. image:: https://flat.badgen.net/https/ucsc-ci.com/api/v4/projects/3/jobs/artifacts/master/raw/badges1.2/required.json%3Fjob=cwl_badge?icon=commonwl&label=CWL%201.2%20Conformance
+   :alt: Toil CWL 1.2 Conformance Badge
+   :target: https://github.com/common-workflow-language/cwl-v1.2/blob/main/CONFORMANCE_TESTS.md
+
 .. image:: https://badges.gitter.im/bd2k-genomics-toil/Lobby.svg
    :alt: Join the chat at https://gitter.im/bd2k-genomics-toil/Lobby
    :target: https://gitter.im/bd2k-genomics-toil/Lobby?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge

{toil-8.0.0.dist-info → toil-8.1.0b1.dist-info}/RECORD

@@ -1,17 +1,17 @@
-toil/__init__.py,sha256=v0u19Zmd-JKCWBr2jn8Eal4oXMOm-sY5MSSnqUIhfH8,19300
+toil/__init__.py,sha256=lOuyAgzwG9OmmOOqvxMOQCUfDU50sudUjUlHvp3aHns,19330
 toil/bus.py,sha256=Hi2TTCVGX4WTw67BOKo7l9yZw9Ln_zcobJzQxrfge4M,29938
-toil/common.py,sha256=EwIN1Ith42OJsSknXwVk7tZ3SFyuHne13_jPZUxP6WE,75521
+toil/common.py,sha256=MR-AUVmQhNHmN1IqlXTHMNzAbMA8JvwDfXzcgxJCjJ8,81333
 toil/deferred.py,sha256=2ShsuPqDwu0jhBQ6ocMwe4lfNegBm2lj7dOG9E7X3Zc,14152
 toil/exceptions.py,sha256=oL2d9uutwtcPkMcEUGrixKUd4y1JLSA0-N7hNJqCLSk,1883
-toil/job.py,sha256=Bpj5bi5NPzkUMrG4mbEbkFHHWheqZwZbGRHAtKFZPWw,173199
+toil/job.py,sha256=w31q56P7pq6yvJpoH6mTQU3l0GBsm_O0jnDi5zpGQqI,173735
 toil/leader.py,sha256=ubIdkEUb3hmGAc7oCWnKuvxOAlyyvOgVyDCN4i6DJAw,85101
 toil/realtimeLogger.py,sha256=2O4AUaKtvItzzCAQKORIEHZ2cDoLf_6njoKWv_uzdFc,9878
 toil/resource.py,sha256=PlI6R28aYqfYLDsztjlAYpkVGfSr2O0DhrgDXpXJxa0,25650
 toil/serviceManager.py,sha256=GE5IUjQmNrekYv9tclim0RlCFf4ueOQ2H4qHjMBrOcg,19978
-toil/statsAndLogging.py,sha256=Nq4bwpieQVmJNpj6vuN8zdM_yVRA2pKpcJGcxOn7SWI,17152
+toil/statsAndLogging.py,sha256=JXir7TCV8OdDaAdt3VsDR2rbdNWk4ILyOwlKHVdoXT0,18696
 toil/toilState.py,sha256=DD52XQv8wRCYzF7-F6Olqa_k6u-_py-JWyjqJHRh6Z0,17989
-toil/version.py,sha256=0ff-z3yLFu7Q8r18rieIWcRnUVqARJPAA8YN_omkeTc,488
-toil/worker.py,sha256=-V5aL9-5fq2muPZKGKix_D81R5bJrRjQ4fuHzyEq9WM,35998
+toil/version.py,sha256=_Xxx7pjBP8pHk7CZP_gx3EuetyVeDsi9SWhpZw7Ux3s,494
+toil/worker.py,sha256=ywdN4v8qz5CuNQgMJcOlOsVj7BcdqdWuoTp6mFCnE0Y,38967
 toil/batchSystems/__init__.py,sha256=T8psI5GmvE71_XmajKsfeQ3YUs6XM7rX1Fy9VNUX_-Q,1036
 toil/batchSystems/abstractBatchSystem.py,sha256=h8mbA_k_7EZqOrbcdQmKHDcAy6D2ZB77XXS3Wu4-E90,33542
 toil/batchSystems/abstractGridEngineBatchSystem.py,sha256=yR3nlCvJRcxYEDRyA3qYuNjvgmVDfzvW4bx9RY14TLg,24336
@@ -24,10 +24,10 @@ toil/batchSystems/kubernetes.py,sha256=5bC_ipdfgIzl2_I1SxqrcRHPjbcicBNznNK2c3u0g
 toil/batchSystems/local_support.py,sha256=R-DT_G5jcQXjZyDQ9OdFj0KUeULMSmcLBen3p-tSGdw,3893
 toil/batchSystems/lsf.py,sha256=rQJe6dpnqs-LAZ0qaAo94VtxvhADwv8XzRTrQulp-mQ,18089
 toil/batchSystems/lsfHelper.py,sha256=IE5y-x-Mofau7jksWjBdTLt5dVvyj-w8dd3gqwZ-r8o,7227
-toil/batchSystems/options.py,sha256=qA6cIFIviI-5ogKwUaTHQkmVnJ7qzsNts8kI3xc49XU,8110
+toil/batchSystems/options.py,sha256=HZ4nI2paKxulcWOd81R3p_j7BE4j2U9ZjWehDKaoyaA,8155
 toil/batchSystems/registry.py,sha256=eizqlhn4AdBzykdOFu_S5ZcU4eYpMB_vDTb8ml6W3Kw,6701
 toil/batchSystems/singleMachine.py,sha256=5qj9gr0bcT8RciNYM_eC-aHORdDSbdM4SGlam1SGlGw,40348
-toil/batchSystems/slurm.py,sha256=oaP_4axl2YBAWFSoK7khAwPCaTVihJTxtP2VRZQ-vn4,37000
+toil/batchSystems/slurm.py,sha256=xwipLljyzCy8IIXoK-bHCrI05FtGqvMCtUFpE-LnBU4,43565
 toil/batchSystems/torque.py,sha256=A3Pe1IvIltpJSoVulfEUrilr-Ok_8E9hf41jbHYYzjQ,11795
 toil/batchSystems/mesos/__init__.py,sha256=jkeRf24eXeOTdRibDzJtqKwXup47FseQS0UXKriKrxg,3554
 toil/batchSystems/mesos/batchSystem.py,sha256=-3COwXjaibZClIHfAgj98SVy2R2yK8UUCjWaOj-R0hM,40194
@@ -36,7 +36,7 @@ toil/batchSystems/mesos/executor.py,sha256=ETsWkx0JaERw7YS5rzv23_xj492hKSxDOsanV
 toil/batchSystems/mesos/test/__init__.py,sha256=qa4iDR9yGhZyViSvTyPH5wi6qIlKpKcC5-bj3uvB4PY,4718
 toil/cwl/__init__.py,sha256=lfyX1eoJ1IA26AUzUl6-ODTi0ZqD_0F6-rL5eqfl_9E,2131
 toil/cwl/conftest.py,sha256=R6Jw5-PeTCK0rapfHmV_VJwVcqlVbO5w3cFUbaIWUnk,848
-toil/cwl/cwltoil.py,sha256=aHc1lqQd9sPaJshg4A--qtkH9pyBAB8XpQfRH14vkU0,181589
+toil/cwl/cwltoil.py,sha256=W7hekJoRG7K1VqRsWDS4In82iHy6Tte2vRdEy0zvdzA,182689
 toil/cwl/utils.py,sha256=CV69GfCEJ1uvAlbDPJKq42Ed19vBE2E5F7v5MZJK7Gw,8023
 toil/fileStores/__init__.py,sha256=xbcTdb31JXsLPxBbL3P5lm8XZlHNBohHPyawXNnZLOs,2388
 toil/fileStores/abstractFileStore.py,sha256=g_gViwfPqYOjGOTQCXrHOulQanump6P0SPirvX6ZqWQ,30851
@@ -49,7 +49,7 @@ toil/jobStores/fileJobStore.py,sha256=r8rymME47BTjGW5a_kb1QDTWF4MDGNrrXtAc8qwpfI
 toil/jobStores/googleJobStore.py,sha256=xcBWTsM35MyfzYwGZJmqBXOTFMBFHTUFDO0tqc5ALgY,24414
 toil/jobStores/utils.py,sha256=R1NKkyHC9txT7KMXAoa51aNOJJOHx7HloPqI7PD6ipA,15521
 toil/jobStores/aws/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-toil/jobStores/aws/jobStore.py,sha256=jJkYnNESOJbGYZ-eydFQjKSxWAe3p9dkXx8r0NQSTPg,88359
+toil/jobStores/aws/jobStore.py,sha256=bx3HIxUX52ynzFVgr-ytOWjdCKE_LoqCtB6BraN8zRU,89914
 toil/jobStores/aws/utils.py,sha256=GDSNhcwgkhyrq1YDdYJscg1gjFyGpGxIARUYH3cMvPw,20584
 toil/lib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/lib/accelerators.py,sha256=HgDO5rgz-9tU_-fLfScABliMH3VdYSVt-juKfQsUenQ,7937
@@ -57,54 +57,58 @@ toil/lib/bioio.py,sha256=lB9fuyOjWtNZfQCc4x2WzGK3x3xDaq6kW8Ghj1wOchc,2384
 toil/lib/compatibility.py,sha256=pPPTJyk3GUZ8SdAv14a3v2HLWbNtcnsAFuCEbh36UZ4,1535
 toil/lib/conversions.py,sha256=CuOHhxpS8RFdp9U-oLSWmhSNLMKT7lqG5N5uhvxfCK4,5135
 toil/lib/docker.py,sha256=IUWvImtzdaPrCqhzVmTrknXXpgPef23DLUsslZ7KInE,20036
+toil/lib/dockstore.py,sha256=vg82P_g3awPz99dOGXt0k4yeJPlJkTfqPHLzyGujKrc,12848
 toil/lib/ec2.py,sha256=gceJSDOlhiD0jtKs0e7rS8ploctt-fhJHzrYHr1_lcw,25570
-toil/lib/ec2nodes.py,sha256=uydhQaTlr_ISjb658MWocL5CRhbzJb6T-OqqylkC-Q0,14668
+toil/lib/ec2nodes.py,sha256=UVlJqVvMofRUhoEpND3Tal5p_p-p5_LHOJRA3dH7ziI,14693
 toil/lib/exceptions.py,sha256=lj9oMa1B10TDeJ-7-xgL48Qrx6PExNrLUE2ZCdWQ2BQ,2946
 toil/lib/expando.py,sha256=JN8dbYk5K48Dwmvb_3bCkO6NYbb89iL0CRchg3_FyFA,2924
 toil/lib/ftp_utils.py,sha256=VqrstWP6dKJnTHtrxGPp7dzeDpyaD4IR4I5NKrPR3g0,7598
 toil/lib/generatedEC2Lists.py,sha256=pcdygnoZLokhhihbzm3YMNtXsNZSsvrhjYFA784qeag,274723
+toil/lib/history.py,sha256=oeUsiB18dRz4D8NpIiCwlnKSChpXaij7iEZRU26MZ4M,43694
+toil/lib/history_submission.py,sha256=upoAYlcUg7_fRbfp90reniKZj_mC_eaafm1kAEjosBk,28014
 toil/lib/humanize.py,sha256=6uXOB07rvAxO8jpIh2kPwy9bfoDu0eEUmBGz9m1chS8,1267
-toil/lib/integration.py,sha256=vCFKjV-2K3T1LCZMqdgfCWDF4FAenGqTSflG_reg4vk,16163
-toil/lib/io.py,sha256=NX3bm7YGsxb6p76sVnRigweFZf12pfA-oXUs23l023U,12328
+toil/lib/io.py,sha256=enIHHdUNsHx8iIT7lrCd6CXMH8s3dTIIMchl0FF4rHY,13001
 toil/lib/iterables.py,sha256=gLbbxBzB0f-hhMRcCN9P-TDqNYK0myUKVCYBa9eJo-c,3459
 toil/lib/memoize.py,sha256=2ikkIOXfZv7LGsoEn8i2ojYTqqNmIIBhSCfBQxySIKg,3225
-toil/lib/misc.py,sha256=jCSSftkKiam_MrH9jAZKMMTBEH9CjTBiUUF8zernll0,6657
+toil/lib/misc.py,sha256=qjtya6l4lwYwzuaVy75CUlGwehWglumh76g2YentvZk,7354
 toil/lib/objects.py,sha256=3XNMtBkNcIB2EMl5cteVDkuSRKAOpnd_GhxgTGVh43M,5381
 toil/lib/resources.py,sha256=KkfM3hSUwTT__Avh8jPxM0VlrXvqajGjnXScMSlqT7Y,4005
-toil/lib/retry.py,sha256=JFGxvx4BK981hqo4MvKoBX1KvJIVNxQafKEYx9MVEDE,22927
+toil/lib/retry.py,sha256=h95XV6zyOsaoTbfNZyPiSjzKL-Cw7HCKaDx37ikO08s,23020
 toil/lib/threading.py,sha256=cdhEqrScvdtCELE0RUukXdV1nlyAlu-ya7DyVSbskrI,30921
 toil/lib/throttle.py,sha256=ua21juOmGI7JZP4pXdR8-s2TpF6PpwW3sg11a2gcrbI,4955
+toil/lib/trs.py,sha256=IK-I-wniAp8oUenit_BlVlGENEq4EukJ18Rr1-edTlI,18882
+toil/lib/web.py,sha256=9eJQteiGfh721crY9CSH4zNpPeH4dylPJ7IarAlSAMo,1432
 toil/lib/aws/__init__.py,sha256=VI77J2o4IehFBpEUjS4eHmXlxEplFnKYHq6w8ZyotEk,7905
 toil/lib/aws/ami.py,sha256=SD728qocULXqWZmxPslcymukG-MxfNniMsBE9d1VVcM,9341
 toil/lib/aws/iam.py,sha256=6qNJ6C61XVzbuPX1p-tcnEcabCjIultrVe9MrgcME04,18550
 toil/lib/aws/s3.py,sha256=accn7bSneZttfb91pZR_80gDhCgVX7Z4ZOKOwM-6u9w,1156
-toil/lib/aws/session.py,sha256=xWtzP52v_Wf0hYTVnoIf0FrL-isXIgzZrwRPeW8ajnI,14543
-toil/lib/aws/utils.py,sha256=CFgg4g3f6I8kIyg8_JB18xzR5yk-WHZXk7cq_NXb_aU,19738
+toil/lib/aws/session.py,sha256=96l_AGsyA3CpTJiOqPemuLWtGsV28K4DU6vjtDR-pxA,15033
+toil/lib/aws/utils.py,sha256=gk75XIj1Nlw8fN_KoaRb8n-rONmAtAuF2wYUqiev_2E,22205
 toil/lib/encryption/__init__.py,sha256=HP19EUYJeIMdjZq11fLn_dXIGU98sIkpTxvMxvPaUSs,705
 toil/lib/encryption/_dummy.py,sha256=6e2fthd6YdgFUgY0kjGb2052KLWUeXD_ejeoCTAThLU,1082
 toil/lib/encryption/_nacl.py,sha256=_EL8LrF5T5DT0dhNIlyIxDB8c8irGe9nJVh1Sn7mFkA,3747
 toil/lib/encryption/conftest.py,sha256=jCrRo2AtsGaO6hitm-wkNOTAU78JWSVA52E0hZdMpq8,227
 toil/options/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-toil/options/common.py,sha256=fNAOlnsLD_2on6gWHV8nTVikzlx_nrhaco6hLLlRbHo,45075
-toil/options/cwl.py,sha256=r2eMuOxbJaq8_mc25KLzzEjAvvWJqe2QfLHcXKidurg,13600
+toil/options/common.py,sha256=c1RtkeeZYw94R-aI_aV6eupvqjYuwBstSBzErHMGs3k,46011
+toil/options/cwl.py,sha256=-KdV5S345Ry-DzmngP_8nHTByeC5UKzEa48Fz-a_1vg,14002
 toil/options/runner.py,sha256=7DxJLvcMm6CLwTZnPW1f9UmQKx1vw5Sq8VaqJDLzC7g,2388
 toil/options/wdl.py,sha256=PJ5qile1zus-Jwld8Sb3KmG8zzIIuYVJMj-8jmaRB6U,3167
 toil/provisioners/__init__.py,sha256=Z3OV95yx77LBVRUtjX_J8r_0OSC2glAIo5y7irbB-S0,9794
 toil/provisioners/abstractProvisioner.py,sha256=R3OuUV2p8GWWuRs2PbaHkjHufOLyoknUaHq4vKPVGMc,58000
 toil/provisioners/clusterScaler.py,sha256=9FgnSPbn2U_FYUSJUeN67A0kdh-Yl0roi5nZLeJVr_I,64980
-toil/provisioners/gceProvisioner.py,sha256=I0g5oNwsRAr3D-gimCIhk6xZZ-HB_Y3jzgOhMRGx86k,24182
+toil/provisioners/gceProvisioner.py,sha256=8OsbSZeMgAB9l03zQ9WdKZ2-zFrHyzgXoLNdGKjdYcU,24212
 toil/provisioners/node.py,sha256=RFLXufNQhjiHUO5fBfbEBd4cbtSUWsNmiGcDDodioMI,15198
 toil/provisioners/aws/__init__.py,sha256=XmVkSuHGMvaMbDJ36yZHGkH5fsUJYJyi3V4R9MYw0Gs,8621
 toil/provisioners/aws/awsProvisioner.py,sha256=Fd2twLvxKeDKfPw-HoxOdgtJqLajwVVJ1VqhDqt-D0I,89097
 toil/server/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/server/app.py,sha256=Xi8ZYs0qKsg1ISNETiYjMtt_qxrou3NuHZcx9bu3MNU,7048
 toil/server/celery_app.py,sha256=PbdwRb7tY5MU4PkPgFZkq7CMiCe6LHBxw5YgcbdsKIE,663
-toil/server/utils.py,sha256=hSeRcdBMBkvS3iGRtF3jB5lVNcsTXJGS-7fV8czuJ4E,21919
+toil/server/utils.py,sha256=HLZb3-HtHqf5QYP3rlSK6C-Av_YxexYrYCcwrcmDP_0,21942
 toil/server/wsgi_app.py,sha256=3V3xr80F4uJUzeBbTbPI1uKJ3FUcI-H_8T1eiiEM5iw,1959
 toil/server/api_spec/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/server/api_spec/workflow_execution_service.swagger.yaml,sha256=zZ2QepvbpvLROIcVIHWrcQLUwXEqGfm68fmkdrx8rw8,25377
 toil/server/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-toil/server/cli/wes_cwl_runner.py,sha256=vw3KKnoe_oof6PLxiJWenHev53YwVmpzc8N9FwZMoKk,18501
+toil/server/cli/wes_cwl_runner.py,sha256=WpvQeO-4LfnXlgcSuPaoZU0owoLFAdzraF86TfHi6m0,18526
 toil/server/wes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/server/wes/abstract_backend.py,sha256=d8IA2Fepwr9g6BU-CO3VBvODiPswsps9rPcOKUUvD8k,10202
 toil/server/wes/amazon_wes_utils.py,sha256=xRrV7hiWoWVwxJykgL2HQdMf1FZg73eqEBltKXya1Fc,10287
@@ -116,7 +120,7 @@ toil/test/batchSystems/batchSystemTest.py,sha256=hMp5mmtGdWxnb4DIjCxy4m-BU9BeJ6n
 toil/test/batchSystems/batch_system_plugin_test.py,sha256=KUVDjbXgxopEqTC4pAAwUePc-QrThxhChyaernYVpVM,2802
 toil/test/batchSystems/test_gridengine.py,sha256=kZCF7WIAmCF1LTPPWd4zC6piQr0UaKJ3kYKz5tsBal0,6353
 toil/test/batchSystems/test_lsf_helper.py,sha256=JICnAPvU7HfqJ0RhIpC-IFfHLKftOAAQF2Iqc7nFs30,4697
-toil/test/batchSystems/test_slurm.py,sha256=bCwVanzQf17c9IY9-bSiDAje1lHyCt2PUWUJZy9GKV4,19529
+toil/test/batchSystems/test_slurm.py,sha256=L1OXdVCHTMPrIsqzeJ8ckf9qdWjfW3qFokHJue-fWts,27473
 toil/test/cactus/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/test/cactus/test_cactus_integration.py,sha256=4sRlsm7b29a08HNHFUbFu_gDW36TQeTfGBvRYUXNF_U,2219
 toil/test/cwl/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -125,8 +129,8 @@ toil/test/cwl/colon_test_output.cwl,sha256=8evFOnHvpJEPn1lBI2zuEKueMUbh2p8oSNOKl
 toil/test/cwl/colon_test_output_job.yaml,sha256=BbXFRuWsRJV6JpJAutnHywJl_AbwEcwNRszArfRecxs,72
 toil/test/cwl/conditional_wf.cwl,sha256=SAtUSmD5ta-DVG0SRHpT8EtOp8ztm-6v9Vskcl09c3s,357
 toil/test/cwl/conditional_wf.yaml,sha256=WsS9dlpbRUll9M56KspQdOJ8h6SASTW7eRELefa274E,24
-toil/test/cwl/conftest.py,sha256=okwzv8y-qDSIz--eauonzQXxj6DxyT-u8sXIUMmjxlE,698
-toil/test/cwl/cwlTest.py,sha256=t98io1NVD1LSwXRT8jzaLH97noUq5Hf2XDJQ34NZ6fc,63465
+toil/test/cwl/conftest.py,sha256=TGB6svRjbKfzieJDrFN6v-Q0MkV94ABGewyFnAr9YSs,1999
+toil/test/cwl/cwlTest.py,sha256=HuBDqCruWn7i8dGf-O910WQYEpJm9iThPWA7H0Kr-UE,67296
 toil/test/cwl/directory_from_directory.cwl,sha256=-hjZuUs5fMpKMnbj-FZAgcns4iWsCFJV6Qh7-fsRn1I,556
 toil/test/cwl/download.cwl,sha256=XQvz8or_-k6pwyhgeUeJOew0_b3BeHcF08EaalbySz4,296
 toil/test/cwl/download_directory.cwl,sha256=RdPmElFeHJqXGWVqEqR5VFMmXDiJubhTcM9hIrAhKY4,535
@@ -143,6 +147,7 @@ toil/test/cwl/measure_default_memory.cwl,sha256=ZGVgLpnKNxOobjOEWc7EF-spCrDqhYrB
 toil/test/cwl/mpi_simple.cwl,sha256=xgsOk2yGbAHL3pwtCtxZd6_c9Lopl1xh32dO0D6-Qbc,470
 toil/test/cwl/not_run_required_input.cwl,sha256=DK8CeCEw8thWiqvoRQmFQcZq6I3HLrt_7gzbYk1te-c,836
 toil/test/cwl/nvidia_smi.cwl,sha256=peKLDFC9_0zEt7CoRLCQDtAE5bjfotok8Ljmn1nBVtA,474
+toil/test/cwl/optional-file.cwl,sha256=TD2oq8XlGKXz7ytl5l2DB6Gf8KTCeciTFH8tTmB9NqQ,229
 toil/test/cwl/preemptible.cwl,sha256=BLmrYR3nZX89p1I0-8vGuE-hqKEUbfsuY-CWDcf32BY,304
 toil/test/cwl/preemptible_expression.cwl,sha256=T_90Y6dBe9nDCjp8Hg4dv9xFsaWVsKSHv5nZ2mafBZ8,639
 toil/test/cwl/revsort.cwl,sha256=BDAyPb1Tpkp55I_XIiZ3_7dXzQJxxkXo_2CHSk5lcEw,2023
@@ -165,8 +170,9 @@ toil/test/lib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/test/lib/dockerTest.py,sha256=w9VZ7KHGz3eEdvV9McqT7NgXXWENkizubaEaiPDVeh4,15607
 toil/test/lib/test_conversions.py,sha256=JSwdTRYklpofPV3VANHC7vHZ7WcpEWOZD6G9Tkjd45w,7232
 toil/test/lib/test_ec2.py,sha256=p3GfCgSSLqZQ-oanHk1sdIuP1wVUwQvXKsXzWl5ow0I,4183
-toil/test/lib/test_integration.py,sha256=E87W-WiOqeHbHNou2d8Nb2GOhjH4XTKL9JH8esQpL2M,4634
+toil/test/lib/test_history.py,sha256=PBgtJzzC_0VAil_yofh4TQX3W6jmGHaXR-dt5eDv3Xg,8344
 toil/test/lib/test_misc.py,sha256=X1o4Dw1PcbnS1Y_gTR2q4STwqRjXYjSEUy2Q1BxeijM,2766
+toil/test/lib/test_trs.py,sha256=mcGn3boLFkjS_aPMOS-gwlFd7QcMVM-vpLadBnZb8SE,6918
 toil/test/lib/aws/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/test/lib/aws/test_iam.py,sha256=2YTrL6r0WIybOBFltU0bJ4XOADT6vlRRXfbsvexjBt8,6921
 toil/test/lib/aws/test_s3.py,sha256=NpYO0GnACbGpaKPwM0yeObxqBoFYJv92RUP7VdtompE,3061
@@ -225,7 +231,7 @@ toil/test/utils/toilDebugTest.py,sha256=FlS8_0jKF5d-Y_g4RucRWQDJtUUM6nsjNCrjxVgq
 toil/test/utils/toilKillTest.py,sha256=qMYnMjeqZGxXan8k0ITaK7D80YYVmfdplFDV0LIJ0t4,3494
 toil/test/utils/utilsTest.py,sha256=cHDWs_KOud1nIEQ13M5GNV_SE4rOPAtoCb43MbZD9l8,19513
 toil/test/wdl/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-toil/test/wdl/wdltoil_test.py,sha256=yHLJGkEEet-aLrcAcs15iVvvWxuE4NUYs-v78DKIXqg,40105
+toil/test/wdl/wdltoil_test.py,sha256=7ULpOyDPCO0ObYY2t7nHiHm2Mu7TO1XhLlHquoOuTU0,40105
 toil/test/wdl/wdltoil_test_kubernetes.py,sha256=a45TojDEwksW7MYk1F0KzQdgXJRktQYOsq36CfpBvuo,2818
 toil/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/utils/toilClean.py,sha256=X6Fws6LVqa-ScUITMTomV5iohXa3yz_rAIFnUfXlqZU,1850
@@ -244,10 +250,10 @@ toil/utils/toilStatus.py,sha256=qacxW5lcguvmhUi1b4cjm1acJik0zpsP7CsUuZyX-fo,2042
 toil/utils/toilUpdateEC2Instances.py,sha256=dreH9Vc2qUoc0he5AwqiFmqdOQp3tMmIfkjWm7GS5qE,1295
 toil/wdl/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 toil/wdl/utils.py,sha256=U0TqbVTsap0VdeZjrUf4l71A7Zns-Hkso1B1Zdp2LRk,1316
-toil/wdl/wdltoil.py,sha256=WQY6bJKErqjfLnXVahe8dJmDyW75qdtiwmTuH5_qRtM,239255
-toil-8.0.0.dist-info/LICENSE,sha256=YVxVi652J1ZDmtC3EMP5r0EbK85-hm_pzogiULmlqUA,12862
-toil-8.0.0.dist-info/METADATA,sha256=B3SObwKGhQzZW2p92CSPbw8dmSWFQP4M45MKedRkl4I,8305
-toil-8.0.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-toil-8.0.0.dist-info/entry_points.txt,sha256=EF2yFhV2UYuJGr-OjMkUOd3RyOCgRWQbS6XJtBJ25eM,436
-toil-8.0.0.dist-info/top_level.txt,sha256=1ydj7IXvHS9tMT5OVTSSpub6ZOaQeIn3KGCgJqaikF0,5
-toil-8.0.0.dist-info/RECORD,,
+toil/wdl/wdltoil.py,sha256=zlYTgS3cYhpVjCCEF0LgCjj1lMaxXV_64i3cUtwI-d0,240083
+toil-8.1.0b1.dist-info/LICENSE,sha256=YVxVi652J1ZDmtC3EMP5r0EbK85-hm_pzogiULmlqUA,12862
+toil-8.1.0b1.dist-info/METADATA,sha256=vlhUOh-R2Xlue9YJSlAWX_lkBvGCOldmshpGPFy93Pg,8663
+toil-8.1.0b1.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
+toil-8.1.0b1.dist-info/entry_points.txt,sha256=EF2yFhV2UYuJGr-OjMkUOd3RyOCgRWQbS6XJtBJ25eM,436
+toil-8.1.0b1.dist-info/top_level.txt,sha256=1ydj7IXvHS9tMT5OVTSSpub6ZOaQeIn3KGCgJqaikF0,5
+toil-8.1.0b1.dist-info/RECORD,,

{toil-8.0.0.dist-info → toil-8.1.0b1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (76.0.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

toil/test/lib/test_integration.py

@@ -1,104 +0,0 @@
-# Copyright (C) 2015-2024 Regents of the University of California
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import io
-import logging
-import pytest
-from typing import IO
-import urllib.request
-from urllib.error import URLError
-
-from toil.lib.retry import retry
-from toil.lib.integration import get_workflow_root_from_dockstore
-from toil.test import ToilTest, needs_online
-
-logger = logging.getLogger(__name__)
-logging.basicConfig(level=logging.DEBUG)
-
-@pytest.mark.integrative
-@needs_online
-class DockstoreLookupTest(ToilTest):
-    """
-    Make sure we can look up workflows on Dockstore.
-    """
-
-    @retry(errors=[URLError, RuntimeError])
-    def read_result(self, url_or_path: str) -> IO[bytes]:
-        """
-        Read a file or URL.
-
-        Binary mode to allow testing for binary file support.
-
-        This lets us test that we have the right workflow contents and not care
-        how we are being shown them.
-        """
-        if url_or_path.startswith("http://") or url_or_path.startswith("https://"):
-            response = urllib.request.urlopen(url_or_path)
-            if response.status != 200:
-                raise RuntimeError(f"HTTP error response: {response}")
-            return response
-        else:
-            return open(url_or_path, "rb")
-
-    # TODO: Tests that definitely test a clear cache
-
-    def test_lookup_from_page_url(self) -> None:
-        PAGE_URL = "https://dockstore.org/workflows/github.com/dockstore/bcc2020-training/HelloWorld:master?tab=info"
-        # If we go in through the website we get an extra refs/heads/ on the branch name.
-        WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore/bcc2020-training/master/wdl-training/exercise1/HelloWorld.wdl"
-        looked_up = get_workflow_root_from_dockstore(PAGE_URL)
-
-        data_from_lookup = self.read_result(looked_up).read()
-        data_from_source = self.read_result(WORKFLOW_URL).read()
-        self.assertEqual(data_from_lookup, data_from_source)
-
-    def test_lookup_from_trs(self) -> None:
-        TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker"
-        # Despite "-checker" in the ID, this actually refers to the base md5sum
-        # workflow that just happens to have a checker *available*, not to the
-        # checker workflow itself.
-        WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore-testing/md5sum-checker/master/md5sum/md5sum-workflow.cwl"
-        looked_up = get_workflow_root_from_dockstore(TRS_ID)
-        
-        data_from_lookup = self.read_result(looked_up).read()
-        data_from_source = self.read_result(WORKFLOW_URL).read()
-        self.assertEqual(data_from_lookup, data_from_source)
-
-    def test_lookup_from_trs_cached(self) -> None:
-        TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker"
-        WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore-testing/md5sum-checker/master/md5sum/md5sum-workflow.cwl"
-        # This lookup may or may not be cached
-        get_workflow_root_from_dockstore(TRS_ID)
-        # This lookup is definitely cached
-        looked_up = get_workflow_root_from_dockstore(TRS_ID)
-        
-        data_from_lookup = self.read_result(looked_up).read()
-        data_from_source = self.read_result(WORKFLOW_URL).read()
-        self.assertEqual(data_from_lookup, data_from_source)
-
-    def test_lookup_from_trs_with_version(self) -> None:
-        TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker:workflowWithHTTPImport"
-        WORKFLOW_URL = "https://raw.githubusercontent.com/dockstore-testing/md5sum-checker/workflowWithHTTPImport/md5sum/md5sum-workflow.cwl"
-        looked_up = get_workflow_root_from_dockstore(TRS_ID)
-        
-        data_from_lookup = self.read_result(looked_up).read()
-        data_from_source = self.read_result(WORKFLOW_URL).read()
-        self.assertEqual(data_from_lookup, data_from_source)
-
-    def test_lookup_from_trs_nonexistent_version(self) -> None:
-        TRS_ID = "#workflow/github.com/dockstore-testing/md5sum-checker:notARealVersion"
-        with self.assertRaises(RuntimeError):
-            looked_up = get_workflow_root_from_dockstore(TRS_ID)
-
-